plot_phastcons_profiles
plot_phastcons_profiles is used to plot conservation profiles based on PhastCons scores from an
index created with format_genome. For each Biopiece record in the stream containing chromosome
coordinates, these are used to lookup the PhastCons score for this loci in the specified genome.
Default graphics are crufty ASCII, but you can get high resolution postscript or SVG output instead
using the -t switch. Plotting is done using GNUplot which allows for different types of output
the default one being crufty ASCII graphics.
GNUplot must be installed for plot_chrdist to work. Read more here:
... | plot_phastcons_profiles [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-g <genome> | --genome=<genome>] # Genome from which to obtain PhastCons info.
[-m | --mean] # Calculate a mean profile.
[-M | --median] # Calculate a median profile.
[-f <uint> | --flank=<uint>] # Include flanking PhastCons scores.
[-t <string> | --terminal=<string> # Terminal for output: dumb|post|svg - Default=dumb
[-T <string> | --title=<string>] # Set plot title - Default="PhastCons Profile"
[-X <string> | --xlabel=<string>] # Set x-axis label.
[-Y <string> | --ylabel=<string>] # Set y-axis label.
[-L | --logscale_y] # Set y-axis to log scale.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
To plot the distinctive four humped camel profile of H/ACA snoRNAs from the Drosophila genome,
we read in the H/ACA snoRNAs BED entries using read_bed
using the -M switch to get the median:
read_bed -i snoRNA_ACA.bed.gz | plot_phastcons_profiles -xMg dm3
PhastCons Profiles
1 ++-***********-------------**********-----------*****--------*******-++
| * ** ** ** * * * * |
0.9 ++* * * * * * * * ++
| * * * * * * * * |
0.8 ++* * * ** * * * *++
| * * ** ** **** * * * |
0.7 +* * * ** *** * * *++
|* * * **** * * * * |
0.6 +* * * * ** * * * *++
0.5 +* * * * * *++
|* * ** * * * |
0.4 +* * * * * *++
|* * * * * * |
0.3 +* * * * * *++
** * * * * * |
0.2 ** * ** * *** *++
* *** **** * |
0.1 *+ ** *++
* |
0 ++-----+------+------+------+------+------+------+------+------+-----++
0 20 40 60 80 100 120 140 160 180 200
To generate a postscript image:
read_bed -i snoRNA_ACA.bed.gz | plot_phastcons_profiles -xMg dm3 -t post -o phastcons_profile.ps
And the result will look like this:
If you choose -t svg instead of -t post the output will be in SVG which is
neat since it can easily be modified using e.g. Inkscape to apply labels and such.
Read more about Inkscape here:
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
plot_phastcons_profiles is part of the Biopieces framework.